Welcome

Welcome to the jPREdictor project. The program was developed foremost for the prediction of cis-regulatory elements. Short sequence fragments, namely transcription factor binding sites, are known to be enriched and clustered in such elements. These binding sites are represented as motifs and for the prediction, they must be known. Using these motifs, it is possible to search them on sequences, to weight them by applying a positive or negative training set (model or background, respectively) and to score a sequence. Please refer to the manual on how to use the program for the prediction of regulatory elements. With version 1.22, two new applications were incorporated into the jPREdictor: motif discovery via motif evolution and the motif clustering. Both tasks can only be started via command-line. Please refer to the manual again to get a brief description on how they function and how they are invoked.

Getting started

You can work with the program in three ways:

• Run the program locally in Java's Webstart environment (recommended).

• Start the program within your browser as an applet. Note, that it also works locally.

• Download the Java program and start it either with a GUI or as command line interpreter.

Current version

Since 24. Apr 2008 version 1.23 of the jPREdictor is available. Some changes were made to the program, and the motif discovery via evolution and the motif clustering is finally official. Please refer to the history section for further explanations on changes and improvements.

We are interested in you and your work

... and your feedback is highly appreciated. We would like to hear about your work group and what the jPREdictor is used for in your group. To do so, please fill in the contact form (the id to use is 'bibiserv_jpredictor') or send us an email. Thank you very much.